Hi Bernhard It has been pointed out to me that my reply was not totally clear on this point, especially to those who haven't followed up the link I sent. By 'output' from a program I mean simply a physical file written when that program is run (i.e. every program has inputs and outputs), so I ought to have said 'output file' to be absolutely clear.
Obviously the data in that output file will be carried through to further programs down the pipeline and will be either copied or massaged in some way, so you could also consider those data to be 'outputs' from the program that first generated them. However I don't think this is a helpful viewpoint: for example the reflection indices are data that were originally generated by the indexing program (e.g. XDS) which are carried through to every subsequent file, but I don't think it's helpful to think of every one of those files to be an 'output' from XDS! I think the best way to make the distinction is to talk about 'files' (physical entities) and 'data' (abstract entities that can be passed from one file to another), so then one has to take care to distinguish 'output file' and 'output data' (which I admit I didn't). If one makes a copy of a file one gets a different file (it has a different filename, location on disk etc.), nevertheless it contains the exact same data. In this case one cannot use the output file from STARANISO for the reason you indicate: the file contains two integer columns (test-set flag and SA flag) and PDB deposition gets confused about which one is the test-set flag. Fortunately the SA flag is only needed to remove the 'unobservable' reflections generated by UNIQUIFY so they don't get 'filled-in' with DFc by a refinement program (e.g. REFMAC). So the SA flag column can then be removed. The link recommends, among other things, that you combine the output file from STARANISO with that from REFMAC to get the map coefficients and in the process drop the SA flag column along with anything else that's not needed for deposition. Cheers -- Ian On Mon, 15 Jul 2019 at 22:59, Ian Tickle <[email protected]> wrote: > > Hi Bernhard > > Oh dear, yes that's quite possible. > > But in any case we recommend _not_ to deposit the output from STARANISO: > > http://staraniso.globalphasing.org/deposition_about.html > > Cheers > > -- Ian > > > Cheers > > -- Ian > > > On Mon, 15 Jul 2019 at 22:40, Bernhard Rupp <[email protected]> > wrote: > >> Hi Fellows – >> >> >> >> wondering if there is a particular reason the PDB cannot process a mtz >> file that in addition to FreeR_flag includes a SA_Flag column from >> StarAniso? >> >> Can there be no more than one I column type because that is automatically >> interpreted as the free flag?? >> >> >> >> Best, BR >> >> >> >> ------------------------------------------------------ >> >> Bernhard Rupp >> >> Crystallographiae Vindicis Militum Ordo >> >> http://www.hofkristallamt.org/ >> >> [email protected] >> >> +1 925 209 7429 >> >> +43 676 571 0536 >> >> ------------------------------------------------------ >> >> Many plausible ideas vanish >> >> at the presence of thought >> >> ------------------------------------------------------ >> >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
